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Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc 2021; 16:3802-3835. [PMID: 34215862 PMCID: PMC8647621 DOI: 10.1038/s41596-021-00556-8] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/14/2021] [Indexed: 02/06/2023]
Abstract
Advances in multiplexed imaging technologies have drastically improved our ability to characterize healthy and diseased tissues at the single-cell level. Co-detection by indexing (CODEX) relies on DNA-conjugated antibodies and the cyclic addition and removal of complementary fluorescently labeled DNA probes and has been used so far to simultaneously visualize up to 60 markers in situ. CODEX enables a deep view into the single-cell spatial relationships in tissues and is intended to spur discovery in developmental biology, disease and therapeutic design. Herein, we provide optimized protocols for conjugating purified antibodies to DNA oligonucleotides, validating the conjugation by CODEX staining and executing the CODEX multicycle imaging procedure for both formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues. In addition, we describe basic image processing and data analysis procedures. We apply this approach to an FFPE human tonsil multicycle experiment. The hands-on experimental time for antibody conjugation is ~4.5 h, validation of DNA-conjugated antibodies with CODEX staining takes ~6.5 h and preparation for a CODEX multicycle experiment takes ~8 h. The multicycle imaging and data analysis time depends on the tissue size, number of markers in the panel and computational complexity.
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Affiliation(s)
- Sarah Black
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Darci Phillips
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - John W Hickey
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Kennedy-Darling
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Akoya Biosciences, Menlo Park, CA, USA
| | - Vishal G Venkataraaman
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nikolay Samusik
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Becton Dickinson, San Jose, CA, USA
| | - Yury Goltsev
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian M Schürch
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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Kennedy‐Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP. Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. Eur J Immunol 2021; 51:1262-1277. [PMID: 33548142 PMCID: PMC8251877 DOI: 10.1002/eji.202048891] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/21/2020] [Accepted: 02/04/2021] [Indexed: 01/04/2023]
Abstract
Multiparameter tissue imaging enables analysis of cell-cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are spatially restricted, giving clues to biological mechanisms behind tissue homeostasis and disease. Here, we streamlined and simplified the multiplexed imaging method CO-Detection by indEXing (CODEX) by validating 58 unique oligonucleotide barcodes that can be conjugated to antibodies. We showed that barcoded antibodies retained their specificity for staining cognate targets in human tissue. Antibodies were visualized one at a time by adding a fluorescently labeled oligonucleotide complementary to oligonucleotide barcode, imaging, stripping, and repeating this cycle. With this we developed a panel of 46 antibodies that was used to stain five human lymphoid tissues: three tonsils, a spleen, and a LN. To analyze the data produced, an image processing and analysis pipeline was developed that enabled single-cell analysis on the data, including unsupervised clustering, that revealed 31 cell types across all tissues. We compared cell-type compositions within and directly surrounding follicles from the different lymphoid organs and evaluated cell-cell density correlations. This sequential oligonucleotide exchange technique enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging.
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Affiliation(s)
- Julia Kennedy‐Darling
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Akoya Biosciences1505 O'Brien DriveMenlo ParkCAUSA
| | - Salil S. Bhate
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - John W. Hickey
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Sarah Black
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Graham L. Barlow
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Gustavo Vazquez
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Vishal G. Venkataraaman
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Nikolay Samusik
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Becton DickinsonSan JoseCAUSA
| | - Yury Goltsev
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Christian M. Schürch
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
- Department of Pathology and NeuropathologyUniversity Hospital and Comprehensive Cancer Center TübingenTübingenGermany
| | - Garry P. Nolan
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
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